Pprint (Prediction of Protein RNA- Interaction) is a web-server for predicting RNA-binding residues of a protein. The prediction is done by SVM model trained on PSSM profile generated by PSI-BLAST search of 'nr' protein database. The SVM model is trained and tested on a set of 86 non-homologous protein chains with 5-fold cross-validation. It has predicted RNA-interacting amino acids with prediction accuracy 75.53% and MCC value of 0.44 during training and testing.

It takes amino acid sequence in FASTA format as input and predict the RNA-interacting residues. The residues in the query sequence predicted as RNA-interacting residues are colored in red and non-interacting residues are colored in blue. Below the amino acid sequence, residue-wise detail prediction is also given in tabular format. This table contain three columns (i) amino acid residue, (ii) SVM score and (iii) prediction. The prediction result depends on the threshold value specified by the user. The default threshold is set as -0.2. To get prediction with less number of false positives, the user should choose higher threshold. For prediction with less number of false negatives, threshold should be very low.

If you are using this web-server please cite: Kumar, M., Gromiha, M.M. and Raghava, G.P.S. Prediction of RNA binding sites in a protein using SVM and PSSM profile. Proteins: Structure, Function and Bioinformatics. 2008 Apr;71(1):189-94